SNP discovery and characterisation in White Rhino (Ceratotherium simum) with application to parentage assignment

Abstract

The white rhino is one of the great success stories of modern wildlife conservation, growing from as few as 50-100 animals in the 1880s, to approximately 20,000 white rhinoceros remaining today. However, illegal trade in conservational rhinoceros horns is adding constant pressure on remaining populations. Captive management of ex situ populations of endangered species using molecular methods can contribute to improving the management of the species. Here we compare for the first time the utility of 33 Single Nucleotide Polymorphisms (SNPs) and nine microsatellites (MS) in isolation and in combination for assigning parentage in captive White Rhinoceros. We found that a combined dataset of SNPs and microsatellites was most informative with the highest confidence level. This study thus provided us with a useful set of SNP and MS markers for parentage and relatedness testing. Further assessment of the utility of these markers over multiple (> three) generations and the incorporation of a larger variety of relationships among individuals (e.g. half-siblings or cousins) is strongly suggested.

Combining molecular and incomplete observational data to inform management of southern white rhinoceros (Ceratotherium simum simum)

“…Based on the genetic parameters determined in this study, we found that the level of genetic diversity was not as low as might be expected from the historical bottleneck. Means of parameters that described population heterozygosity such as H o , H e , and F is in this study were similar to those found in other SWR genetic studies (Coutts 2009;Guerier et al 2012;Harper et al 2013;Labuschagne et al 2017). The mean H o estimated from microsatellite markers in other SWR studies ranged from 0.440 to 0.478; while average H o found in this study was 0.426.…”

“…Guerier et al (2012) constructed a complete pedigree of a managed SWR population of 31 individuals by achieving 100% assignment rate of both parents for all 23 offspring using a combination of 11 microsatellite loci sampled from all individuals (H e = 0.450, H o = 0.450, N a = 2.8) and wellmaintained historical records. Labuschagne et al (2017) employed nine microsatellite loci (H e = 0.508, H o = 0.478, N a = 2.8) and 33 SNPs (H e = 0.350, H o = 0.357) to confirm maternity of all 11 dam-offspring pairs known from historical records in a managed SWR population; however, paternity assignment could be obtained with confidence for only six offspring. The results of these studies suggested that smaller number of candidate parents and the capacity to sample all individuals in the populations were the important factors to achieve a high assignment rate.…”

“…Sub-territories within the reserve might have developed as a result of the population growing and following the construction of a new waterhole in the reserve that would allow multiple nonoverlapping territories of the bulls. There are few genetic studies that have successfully obtained paternity assignment in SWR populations that would allow researchers to determine the dominant reproductive behaviour of the species because most studies have been unable to assign the paternity of offspring with statistical confidence (Coutts 2009;Labuschagne et al 2017). However, one study conducted in a limited free-ranging population that held two founder bulls reported that the bull that was believed to be subordinate had actually sired 10 of 13 offspring during a 9-year period.…”